HEADER PHOSPHOTRANSFERASE 07-MAY-97 1ZIP TITLE BACILLUS STEAROTHERMOPHILUS ADENYLATE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADK; COMPND 5 EC: 2.7.4.3; COMPND 6 OTHER_DETAILS: ZINC FINGER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422 KEYWDS PHOSPHOTRANSFERASE, KINASE, ATP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.B.BERRY,G.N.PHILLIPS JR. REVDAT 7 22-MAY-24 1ZIP 1 REMARK REVDAT 6 09-AUG-23 1ZIP 1 REMARK LINK REVDAT 5 07-MAR-18 1ZIP 1 REMARK REVDAT 4 24-FEB-09 1ZIP 1 VERSN REVDAT 3 03-MAY-05 1ZIP 1 AUTHOR JRNL REVDAT 2 01-APR-03 1ZIP 1 JRNL REVDAT 1 20-AUG-97 1ZIP 0 JRNL AUTH M.B.BERRY,G.N.PHILLIPS JR. JRNL TITL CRYSTAL STRUCTURES OF BACILLUS STEAROTHERMOPHILUS ADENYLATE JRNL TITL 2 KINASE WITH BOUND AP5A, MG2+ AP5A, AND MN2+ AP5A REVEAL AN JRNL TITL 3 INTERMEDIATE LID POSITION AND SIX COORDINATE OCTAHEDRAL JRNL TITL 4 GEOMETRY FOR BOUND MG2+ AND MN2+. JRNL REF PROTEINS V. 32 276 1998 JRNL REFN ISSN 0887-3585 JRNL PMID 9715904 JRNL DOI 10.1002/(SICI)1097-0134(19980815)32:3<276::AID-PROT3>3.0.CO; JRNL DOI 2 2-G REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 15235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1524 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1687 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.985 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.413 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177489. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-96 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1AKY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.9 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.20000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 108 -63.72 -91.60 REMARK 500 HIS A 142 74.54 -161.92 REMARK 500 GLU A 198 58.07 -95.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 219 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 CYS A 133 SG 117.3 REMARK 620 3 CYS A 150 SG 104.8 104.4 REMARK 620 4 CYS A 153 SG 98.5 116.2 115.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 220 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 A 218 O2B REMARK 620 2 AP5 A 218 O2G 82.9 REMARK 620 3 HOH A 300 O 169.5 86.8 REMARK 620 4 HOH A 301 O 105.6 170.3 84.8 REMARK 620 5 HOH A 302 O 86.7 92.2 91.8 93.0 REMARK 620 6 HOH A 303 O 89.0 94.4 93.7 81.3 171.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZF REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZINC FINGER RESIDUES. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 218 DBREF 1ZIP A 1 217 UNP P27142 KAD_BACST 1 217 SEQRES 1 A 217 MET ASN LEU VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 A 217 GLY THR GLN ALA GLU LYS ILE VAL ALA ALA TYR GLY ILE SEQRES 3 A 217 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA MET SEQRES 4 A 217 LYS GLU GLY THR PRO LEU GLY LEU GLN ALA LYS GLN TYR SEQRES 5 A 217 MET ASP ARG GLY ASP LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 A 217 GLY ILE VAL ARG GLU ARG LEU SER LYS ASP ASP CYS GLN SEQRES 7 A 217 ASN GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 A 217 GLN ALA GLU ALA LEU GLU THR MET LEU ALA ASP ILE GLY SEQRES 9 A 217 ARG LYS LEU ASP TYR VAL ILE HIS ILE ASP VAL ARG GLN SEQRES 10 A 217 ASP VAL LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 A 217 ARG ASN CYS GLY ALA THR TYR HIS LEU ILE PHE HIS PRO SEQRES 12 A 217 PRO ALA LYS PRO GLY VAL CYS ASP LYS CYS GLY GLY GLU SEQRES 13 A 217 LEU TYR GLN ARG ALA ASP ASP ASN GLU ALA THR VAL ALA SEQRES 14 A 217 ASN ARG LEU GLU VAL ASN MET LYS GLN MET LYS PRO LEU SEQRES 15 A 217 VAL ASP PHE TYR GLU GLN LYS GLY TYR LEU ARG ASN ILE SEQRES 16 A 217 ASN GLY GLU GLN ASP MET GLU LYS VAL PHE ALA ASP ILE SEQRES 17 A 217 ARG GLU LEU LEU GLY GLY LEU ALA ARG HET ZN A 219 1 HET MN A 220 1 HET AP5 A 218 57 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 MN MN 2+ FORMUL 4 AP5 C20 H29 N10 O22 P5 FORMUL 5 HOH *202(H2 O) HELIX 1 1 LYS A 13 TYR A 24 1 12 HELIX 2 2 THR A 31 GLU A 41 1 11 HELIX 3 3 PRO A 44 ARG A 55 1 12 HELIX 4 4 ASP A 61 LEU A 72 1 12 HELIX 5 5 ASP A 75 CYS A 77 5 3 HELIX 6 6 VAL A 90 ILE A 103 1 14 HELIX 7 7 GLN A 117 THR A 125 1 9 HELIX 8 8 ALA A 161 ASP A 163 5 3 HELIX 9 9 GLU A 165 LYS A 189 1 25 HELIX 10 10 MET A 201 LEU A 215 1 15 SHEET 1 A 5 LEU A 192 ASN A 196 0 SHEET 2 A 5 TYR A 109 ASP A 114 1 N VAL A 110 O ARG A 193 SHEET 3 A 5 ASN A 2 MET A 6 1 N VAL A 4 O TYR A 109 SHEET 4 A 5 PHE A 81 ASP A 84 1 N PHE A 81 O LEU A 3 SHEET 5 A 5 PRO A 27 SER A 30 1 N PRO A 27 O LEU A 82 SHEET 1 B 2 ARG A 127 ILE A 129 0 SHEET 2 B 2 THR A 136 HIS A 138 -1 N TYR A 137 O ARG A 128 LINK SG CYS A 130 ZN ZN A 219 1555 1555 2.37 LINK SG CYS A 133 ZN ZN A 219 1555 1555 2.28 LINK SG CYS A 150 ZN ZN A 219 1555 1555 2.33 LINK SG CYS A 153 ZN ZN A 219 1555 1555 2.29 LINK O2B AP5 A 218 MN MN A 220 1555 1555 2.34 LINK O2G AP5 A 218 MN MN A 220 1555 1555 2.31 LINK MN MN A 220 O HOH A 300 1555 1555 2.24 LINK MN MN A 220 O HOH A 301 1555 1555 2.13 LINK MN MN A 220 O HOH A 302 1555 1555 2.06 LINK MN MN A 220 O HOH A 303 1555 1555 2.14 CISPEP 1 PHE A 86 PRO A 87 0 0.63 SITE 1 ZF 5 CYS A 130 CYS A 133 CYS A 150 CYS A 153 SITE 2 ZF 5 ZN A 219 SITE 1 AC1 4 CYS A 130 CYS A 133 CYS A 150 CYS A 153 SITE 1 AC2 5 AP5 A 218 HOH A 300 HOH A 301 HOH A 302 SITE 2 AC2 5 HOH A 303 SITE 1 AC3 39 PRO A 9 GLY A 10 ALA A 11 GLY A 12 SITE 2 AC3 39 LYS A 13 GLY A 14 THR A 15 THR A 31 SITE 3 AC3 39 GLY A 32 PHE A 35 ARG A 36 MET A 53 SITE 4 AC3 39 ASP A 57 LEU A 58 VAL A 59 THR A 64 SITE 5 AC3 39 GLY A 85 ARG A 88 GLN A 92 ARG A 123 SITE 6 AC3 39 LEU A 124 ARG A 127 TYR A 137 HIS A 138 SITE 7 AC3 39 ARG A 160 ARG A 171 GLN A 199 MET A 201 SITE 8 AC3 39 MN A 220 HOH A 300 HOH A 302 HOH A 303 SITE 9 AC3 39 HOH A 305 HOH A 315 HOH A 317 HOH A 330 SITE 10 AC3 39 HOH A 363 HOH A 465 HOH A 496 CRYST1 41.200 62.400 41.600 90.00 116.70 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.024272 0.000000 0.012207 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026908 0.00000